# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /augustus/config/ ...
# Using protein profile unknown
# --[8..137]--> unknown_B (16) <--[15..60]--> unknown_D (13) <--[0..37]--> unknown_E (10) <--[0..1]--> unknown_F (12) <--[0..6]--> unknown_G (16) <--[7..11]--> unknown_H (13) <--[0..4]--> unknown_I (16) <--[15..44]--> unknown_K (29) <--[2..16]--> unknown_L (110) <--[0..5]--> unknown_M (22) <--[0..1]--> unknown_N (118) <--[5..12]--> unknown_O (19) <--[0..1]--> unknown_P (43) <--[0..6]--> unknown_Q (10) <--[0..2]--> unknown_R (34) <--[0..1]--> unknown_S (19) <--[0..3]--> unknown_T (7) <--[0..2]--> unknown_U (9) <--[0..8]--> unknown_V (18) <--[0..5]--> unknown_W (16) <--[45..96]--> unknown_Z (19) <--[9..145]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig500620180911_busco_2432604931_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 6087, name = Contig5006) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig5006	AUGUSTUS	gene	1	1474	0.34	-	.	g1
Contig5006	AUGUSTUS	transcript	1	1474	0.34	-	.	g1.t1
Contig5006	AUGUSTUS	intron	199	406	0.41	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5006	AUGUSTUS	CDS	1	198	0.41	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5006	AUGUSTUS	CDS	407	1474	0.34	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5006	AUGUSTUS	start_codon	1472	1474	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggatatgtaccaagtgaggaaaatcacagacataacgacacagaaatgtaggatcgacattcctacactcaggcagc
# tgggggttaagccagcatcatttgcagccatatccatggacagcacagaatacatctgtcaagtctggccaactcaacacgtaacagggactgggata
# ggagtaggcactgcagtctcaaagcatacagatcatgtaaagaaagagaagacgtgtaagattagaccactcgatgttgtaccaggtaaaagtgtcag
# tgtgagcttgattgtgactaaggcagaagatgtgagagtatacagaagattgatgactgagagtgcacagaggttatcggagatctgtcggggactgc
# tgtataaaacctgtatatcctcccactttgttgtggacaaggagacttgtactctggccaaattacatggtatttcccttattctgatagataaagta
# tcggatgataactactgtgttgtggacaacacaacatgtataactgtgaaaatgatacagagcagagaacattatttgcaaaaacagactacagcaaa
# gacaattcctttaggaggcttagataaagttagtgaagagttatttgaatttatatgtttatcctgtagtgaaaaatccacagaaaatagtacattga
# ggctccccaaaggagttctcctacgcggaccaccagggacaggaaaaacgtcgctggtccgaaatgtgtgtatgaaatgtgacgcttttgtaatctcc
# gtaaacggacccgaagtgtttggatcacgtccgggagaaactgaggagaacataacgaaggttttccagaaagcttttctgatgagtgaagagggagc
# ctgtgttgtgtttctggatgaaattgattccttgtgtccgaaaaggggaaattctgacgacaccagtgatacacgatccactagcgtgttcctcgcgt
# atttagacaagatacatgagtataagaatatagctgtgataggggccaccaacagacctgcagctctagatcccagtcttaggcgaccaggacgcctc
# gacagagagatcatgataaatgttcctactcttagtcaaaggaaagaaatactgaaacgtcagtgtactgaattaagagtggactctggtctggattt
# ggaagtgatagctcagatgaccaatggatttgtaggtgctgacttaatgtcactgtgccatgaagcagcatttagagccatgagttctctccagtcca
# gtgttacagaa]
# protein sequence = [MDMYQVRKITDITTQKCRIDIPTLRQLGVKPASFAAISMDSTEYICQVWPTQHVTGTGIGVGTAVSKHTDHVKKEKTC
# KIRPLDVVPGKSVSVSLIVTKAEDVRVYRRLMTESAQRLSEICRGLLYKTCISSHFVVDKETCTLAKLHGISLILIDKVSDDNYCVVDNTTCITVKMI
# QSREHYLQKQTTAKTIPLGGLDKVSEELFEFICLSCSEKSTENSTLRLPKGVLLRGPPGTGKTSLVRNVCMKCDAFVISVNGPEVFGSRPGETEENIT
# KVFQKAFLMSEEGACVVFLDEIDSLCPKRGNSDDTSDTRSTSVFLAYLDKIHEYKNIAVIGATNRPAALDPSLRRPGRLDREIMINVPTLSQRKEILK
# RQCTELRVDSGLDLEVIAQMTNGFVGADLMSLCHEAAFRAMSSLQSSVTE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703YA.prfl --predictionStart=0  --predictionEnd=20988  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig500620180911_busco_2432604931_.temp